The PPM signal OUT of the 368 goes INTO pin 49 (PL0) in the Mega1280 chip. From there, the signal is DECODED via SOFTWARE so you can do whatever you want with the ch1 thru ch8 inputs to the 368 chip.
The 368 chip MULtiplexes the 8 RX inputs and makes the PPM signal for the 1280 chip.
I hope that explains it.
Earl
Since you said "in0-in7" I will assume you are talking about ArduPilot Mega. The hardware failsafe multiplexor operates on in7, however there will be a user parameter in the firmware so that you can set flight mode on any channel you choose. If you do it with a channel other than in7 then it is a software (only) function and does not involve the mux.
Replies
The 368 chip MULtiplexes the 8 RX inputs and makes the PPM signal for the 1280 chip.
I hope that explains it.
Earl